Hello all. I’m just getting started with Stan in python via cmdstanpy. I’m using the associated conda environment, and using the stock regression model in the stan manual (see Regression Models) to get something working before I get more adventurous. I have some replicated dose response experiments, and I’m interested in describing the variation on that level (‘ll’ in the data). I don’t have a full set of doses for some of the reps, but I’m hoping to borrow some information from the more complete reps.
I get the retcode -11 error, which I take to be 139. I’m outputting files to my working directory, and they are empty stdout.txt files. I’m wondering how I should go about starting to troubleshoot this. My data json looks like this:
{"D": 1, "N": 1946, "L": 3, "y": [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0, 0, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 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Here is the model for convenience:
data {
int<lower=1> D; // number of predictors
int<lower=0> N; // number of observations
int<lower=1> L; // number of replicates
array[N] int<lower=0, upper=1> y;
array[N] int<lower=1, upper=L> ll; // replicate designation (1 through L)
array[N] row_vector[D] x; // predictors (dose)
}
parameters {
array[D] real mu; // mean
array[D] real<lower=0> sigma; // standard dev, positive restriction
array[L] vector[D] beta;
}
model {
for (d in 1:D) {
mu[d] ~ normal(0, 100);
for (l in 1:L) {
beta[l, d] ~ normal(mu[d], sigma[d]);
}
}
for (n in 1:N) {
y[n] ~ bernoulli(inv_logit(x[n] * beta[ll[n]]));
}
}
And here is the compiling, fitting, etc.:
my_stanfile = os.path.join('.', 'logistic.stan')
my_model = stan.CmdStanModel(stan_file=my_stanfile, cpp_options={'STAN_THREADS':'true'})
my_model.name
my_model.stan_file
my_model.exe_file
my_model.code()
my_model.sample(data='data.json', show_console=True, iter_sampling=2000,
chains=1, output_dir=os.path.join('.', 'runfiles'), inits=0)
Does anything jump out as super illegal here? Any basic troubleshooting steps would be great since I’m not getting a lot of info to stdout.txt (I guess the error is happening pretty immediately).
Thanks!